LAMMPS (17 Apr 2024)
WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
# test of replicating system with periodic bonds in x

dimension       2
atom_style      molecular

read_data       data.bond.x
Reading data file ...
  orthogonal box = (0 0 -0.5) to (3 1 0.5)
  4 by 1 by 1 MPI processor grid
  reading atoms ...
  3 atoms
  scanning bonds ...
  1 = max bonds/atom
  orthogonal box = (0 0 -0.5) to (3 1 0.5)
  4 by 1 by 1 MPI processor grid
  reading bonds ...
  3 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     2 = max # of 1-3 neighbors
     4 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.003 seconds

#replicate       3 3 1
replicate       3 3 1 bond/periodic
Replication is creating a 3x3x1 = 9 times larger system...
  orthogonal box = (0 0 -0.5) to (9 3 0.5)
  4 by 1 by 1 MPI processor grid
  bounding box image = (0 0 0) to (0 0 0)
  bounding box extra memory = 0.00 MB
  average # of replicas added to proc = 5.25 out of 9 (58.33%)
  27 atoms
  27 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     2 = max # of 1-3 neighbors
     4 = max # of 1-4 neighbors
     6 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  replicate CPU = 0.002 seconds

mass            1 1.0
velocity        all create 0.02 87287 loop geom

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0

bond_style      harmonic
bond_coeff      1 50.0 1.0

special_bonds   fene
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     2 = max # of 1-2 neighbors
     6 = max # of special neighbors
  special bonds CPU = 0.000 seconds

fix             1 all nve

write_data      tmp.data.x
System init for write_data ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 7 3 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d
      bin: standard

dump		1 all image 100 tmp.image.x.*.ppm type type                 adiam 0.2 bond type 0.1 zoom 1.6
dump_modify	1 pad 5

#dump		2 all movie 100 tmp.movie.x.mpg type type #                adiam 0.2 bond type 0.1 zoom 1.6
#dump_modify	2 pad 5

run             5000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Inconsistent image flags (../domain.cpp:1051)
Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0.02          -1.1250229      0             -1.1057636      9.028122     
      5000   0.50911963    -1.7968226      0.21209852    -1.0944607      4.1676488    
Loop time of 0.21682 on 4 procs for 5000 steps with 27 atoms

Performance: 9962160.612 tau/day, 23060.557 timesteps/s, 622.635 katom-step/s
93.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.001787   | 0.0021247  | 0.0028772  |   1.0 |  0.98
Bond    | 0.00039682 | 0.00045617 | 0.00059887 |   0.0 |  0.21
Neigh   | 0.0013626  | 0.0014006  | 0.0014798  |   0.1 |  0.65
Comm    | 0.017009   | 0.01791    | 0.018656   |   0.5 |  8.26
Output  | 0.06892    | 0.12188    | 0.18918    |  13.7 | 56.21
Modify  | 0.00060336 | 0.00072159 | 0.00088047 |   0.0 |  0.33
Other   |            | 0.07233    |            |       | 33.36

Nlocal:           6.75 ave           7 max           6 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost:           64.5 ave          65 max          63 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs:          70.25 ave          77 max          60 min
Histogram: 1 0 0 0 0 1 0 0 1 1

Total # of neighbors = 281
Ave neighs/atom = 10.407407
Ave special neighs/atom = 2
Neighbor list builds = 287
Dangerous builds = 0
Total wall time: 0:00:00
